Abstract 3416: Customizable gene panels overcome challenges associated with targeted resequencing

• Published in: Cancer research (Chicago, Ill.) Vol. 78; no. 13_Supplement; p. 3416
• Main Authors: Barry, Andrew John, Patel, Kruti M., Emerman, Amy B., Adams, Scott, Bowman, Sarah, Mauceli, Evan, Stewart, Fiona, Dimalanta, Eileen, Russello, Salvatore, Elfe, Charles, Davis, Theodore, Hendrickson, Cynthia
• Format: Journal Article
• Language: English
• Published: 01.07.2018
• DOI: 10.1158/1538-7445.AM2018-3416
• ISSN: 0008-5472

Abstract Efficient utilization of targeted gene panels for clinical research is challenged by the wide variation in gene constituents specific to a given study. While focused gene panels efficiently provide the necessary depth of coverage for low-frequency variant detection, the high costs and technical requirements associated with panel design present obstacles to delivering assays that are focused on the specific targets of interest. The NEBNext DirectTM technology utilizes a novel approach to selectively enrich nucleic acid targets ranging from a single gene to several hundred genes, without sacrificing specificity. The approach rapidly hybridizes both strands of genomic DNA with biotinylated probes prior to streptavidin bead capture, enzymatic removal of off-target sequences, and conversion of captured molecules into sequence-ready libraries. This results in an exceptionally uniform coverage profile for a given target. Unlike alternative hybridization methods, this 1-day workflow does not necessitate upfront library preparation, and instead converts the captured molecules into libraries compatible with Illumina sequencing. We have designed and optimized baits specific to the full exonic content of >800 genes associated with cancer as well as a variety of other disease areas. These are designed, balanced, and pooled on a per gene basis, and can be readily combined into customized panels, allowing rapid turnaround of specific custom gene subsets. Here, we present the ability to rapidly deploy custom gene panels across a variety of panel sizes and content, while maintaining high specificity, uniformity of coverage across target content, and sensitivity to detect nucleic acid variants from clinically relevant samples. Citation Format: Andrew John Barry, Kruti M. Patel, Amy B. Emerman, Scott Adams, Sarah Bowman, Evan Mauceli, Fiona Stewart, Eileen Dimalanta, Salvatore Russello, Charles Elfe, Theodore Davis, Cynthia Hendrickson. Customizable gene panels overcome challenges associated with targeted resequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3416.